S109: P53 ORCHESTRATES SPATIO-TEMPORAL EPIGENOME REWIRING TO TRANSCRIPTIONALLY PREVENT MALIGNANT TRANSFORMATION
Authors: François Serra, Monica Cabrera, Llorenc Rovirosa, Andrea Nieto-Aliseda, Lucía Fnalo-Escudero, Alfonso Valencia, Biola M Javierre
Journal: HemaSphere (2023)

Background: Cell stress and DNA damage activate p53 transcription factor, triggering transcriptional activation of a myriad of target genes to ultimately facilitate distinct cellular outcomes, including cell cycle arrest, senescence, or apoptosis among others. However, the molecular mechanisms underlaying p53-related gene transcription regulation are not completely understood. This gap of knowledge is critical since p53 is one of the most frequently mutated gene in blood malignancies leading the loss of one of the first barriers to prevent malignant transformation. Aims: In this project we addressed this gap of knowledge. p53 preferentially bind enhancers. Since enhancers control transcription of target genes though physical proximity with their promoters, proximity determined by the 3D genome folding within the nucleus, we aimed to study the role of spatio-temporal genome architecture in the p53 response. Specifically, we deciphered how p53 activation orchestrate the 3D epigenetic landscape to ultimately control gene transcription and block cancer development. Methods: To study the dynamic crosstalk between spatiotemporal genome architecture, epigenetics and transcription triggered by p53 we have modelled p53 activation on time and performed a multiomics integration of Hi-C, Promoter Capture Hi-C (PCHi-C), ChIP-seq and RNA-seq data. Just to note, PCHi-C is the method that we previously developed to associated distal enhancers and target genes (Javierre et al., Cell, 2016). Results: We demonstrated that p53 drives dramatic changes in genome architecture, including A/B compartments, Topological Associated Domains (TADs) and DNA loops after minutes of its activation. These changes accompanied epigenetic landscape re-configuration to ultimately trigger p53-related transcriptional response. Then, we defined set of functional p53 binding sites, being most of these at enhancers as previously reported. p53 activation drove new-loop formations between p53-bound enhancers and gene promoters. However, in some cases the 3D chromatin topology was pre-established. In both cases, DNA loops allowed the propagation of the activating p53 effect from distal enhancers to promoter to ultimately lead gene transcription upregulation. Specifically, we associated these functional p53 binding sites at enhancers with a set of 331 distal target genes, which in most of the cases were not the closest gene in the linear genome (mean distance between p53-bound enhancers and target gene porters of 153Kb). Among these, we did not only identified examples of previously identified p53 target genes (e.g.TP53INP1, PLK2) but we also identified potentially new direct target genes and pathways distally controlled by p53. Summary/Conclusion: Collectively, our results demonstrate that p53 activation dramatically reshapes the promoter-enhancer interactome landscape to ultimately control the transcriptional response. Besides, this study provides the first set of genes and pathways distally controlled by p53 and suggest candidate non-coding regions (i.e., p53-bound functional enhancers and linked promoters) that can be mutated or epimutated in blood malignancies to lead an aberrant p53 response in a wild p53 condition. Keywords: Transcriptional regulation